Shattered Soul
by UnholyTomahawk
Summary: A dark past. A bleak future. Shinji's past is much worse than the original. With a fragmented heart and a broken soul, how will the future play out? Rating for abuse and adult themes. "You have to promise that you will go on living." Rated M for future content.


**A/N: Hey everybody, and welcome to my new story, Shattered Soul. I have actually been planning this one for a while and have just recently been able to write it down. First Chapter is a bit short, but I hope you all enjoy.**

**Disclaimer: I don't Evangelion or any of its characters. I am merely doing this for fun and I am not looking to, or receiving any profit from this story. **

**Chapter 1: Arrival**

_He stirred lightly as the body next to him shifted. His eyes cracking open as he pulled his arms away from their current source of warmth, letting out a small yawn at the person next to him sat up. _

"_I never can sneak away without you waking up…." She said to him, turning to look back over her shoulder at him as her feet went over the side of the bed and hit the floor, her long blonde hair falling along her back, her body covered in an overly large t-shirt._

_He simply shrugged and sat up himself, stretching and wincing sharply at the pain running through his body, though quickly doing his best to recover and give her a smile. "I'd rather you be the first thing I see upon waking up anyway…" He whispered out, trying to shrug off the concerned look she was giving him._

"_Is it bad this morning…?" He could barely hear her whisper, the overwhelming depression in her voice. His hand moving up and placing it around her as he pulled her to him, her back hitting his chest as he ignored the pain the movement caused him. _

"_It's been worse…." He replied honestly, not even trying to hide anything anymore, his forehead resting against the back of her head as he gave a sigh, cherishing the moment of closeness before he was forced to let her go as she stood up. He looked up at her as she turned around, seeing her green eyes looking down at him with a mixture of happiness and sadness, a strange combination, but one they were both used to._

_They didn't say anything else for several moments; both knowing they didn't have much time before _they_ woke up and fleeting moments such as these would not be possible. She gave him a small smile, nothing needing to be said, both knowing what the other felt at the moment and what needed to be done. Her hand rose up and grazed his cheek gently and he felt himself melt into it before he returned the small smile before she turned to leave. _

"_Someday… Someday it won't be like this…." He whispered out, though not sure if he was speaking to himself or her as he watched her go. Watching her silently open the door to his room and turning to look at him one last time with saddened yet thankful eyes. "Remember to keep your promise until then…."_

* * *

A young man opened his eyes as he felt the train he was currently riding begin to slow down, quickly glancing to the side to see that it was arriving at his designated stop.

"Never fails…." He whispered to himself, remembering the dream he had just woken up to thanks to the train pulling to a stop, not paying attention to the monotone voice that came over the speakers as he stood up and grabbed the only bag he had brought with him, a simple duffel bag with an owner tag with the name Shinji Ikari on it, before stepping off of the train and onto the platform.

Looking around, he watched the few others around him go about their business as he pulled out a card and letter he had received that had started his travel to Tokyo-3. The letter was from his father, though calling the man that was a stretch in his opinion and the card was more of a picture, one of an attractive looking woman with purple hair that had contact information on it. '_Interesting way to give someone contact information.'_ He thought to himself.

He walked out of the station in pursuit of a more available payphone to call the number, all of the ones in the station having been in use. It also gave him an excuse to see a bit more of the city that he had just come to as he walked down the street that the station exited onto. He was dressed casually, a simple white t-shirt with a cool blue overshirt that he left unbuttoned to show the white t-shirt beneath it. A basic pair of jeans finished the outfit, nothing to spectacular. The young man himself looked to be around 16 and had a fairly slim yet athletic build to him with short brown hair and blue eyes. Overall, he appeared to be an ordinary teenager with some decent looks.

He noticed a payphone down the street a ways and made his way to it, grabbing some change he had in his pocket to make a call to the number he had on the contact list, however his plan was cut off at the sound of siren filling the air.

Caught off guard, he looked around with a blank expression, wondering what was going on, but not seeing anyone else in the streets and noticing he didn't quite realize where he had wandered to in his search for a payphone. '_Way to be observant in a new place Shinji…' _He thought to himself as he tuned out the siren and picked up the phone, hoping he could get some answers but only to receive an emergency warning telling him to get to a shelter. _'That would help if I knew where a shelter was…'_ He thought with another sigh before putting the phone back and picking his bag up to try and find out what was going on only to freeze at the sight of an unusual girl standing in the road.

She had light blue hair and red eyes, with a pale complexion and was dressed in what appeared to be some kind of school uniform. He didn't have time to so much as blink before she was gone, leaving him a bit confused.

"Damnit…" He whispered to himself as he looked around some more. "What am I supposed to do? I don't know this city at all…" He didn't have time to think much more on the subject before what sounded like an explosion went off in the distance. He barely had time to turn and look in the direction that he believed the sound had come from before all hell broke loose around him.

* * *

Misato Katsuragi knew the situation was bad. She had been getting ready to head to the station after she had found out that the boy she was supposed to be picking up had arrived earlier than expected due to the train having skipped a few stops along the way. It wasn't long after she had gotten into her car and began to head towards the said station that the alarms and her own cell went off. _'Things would end up going this way.'_ She thought to herself with a sigh before flipping open the cell phone and answering it.

"Yes, I know. I can hear the siren, what's the situation?" She asked without even waiting for the person on the other line to begin, accelerating her car even faster to go and find the boy she had been told to pick up.

"We just picked it up outside the city in the ocean a few minutes ago. The military has engaged but all attacks are ineffective, just as we suspected. It hit land and is quickly moving its way towards the city itself, all main buildings having already been suspended down into the Geofront…."

Misato half listened to the rest of the report, already knowing most of what would be happening as she cursed lightly to herself. _'Despite how far we have come in preparation, we still weren't ready…'_

"Got it!" She yelled into the phone, interrupting the report she was being given as she turned down the street near the station, eyes scanning the surrounding area for Shinji Ikari. "I'm picking up the boy and heading in as soon as I can, be sure to have all possible car trains ready in the immediate area in case the Angel makes it to this area quicker than expected."

She shut the phone without waiting for confirmation, knowing the crew on the bridge well enough that they would get it down. "Damnit…" She whispered out fiercely, turning down another street as her eyes scanned all around, her destination still being the station. "You better be at that station Shinji Ikari!" She yelled out to herself in frustration at the whole situation before hearing the sound of a large explosion in the distance.

"Shit!" She cursed, "Its already made it in this far! I have to find him quick!" Yelling more to herself as she hit the gas even more in her search.

* * *

It happened faster than he thought possible. The sound of an explosion in the distance was nothing compared to what came next. He barely had time to register as what he could only described as missiles went screaming overhead, just barely clearing the roofs of the buildings not 20 feet above him, causing him to grab his ears in pain before they disappeared and the sound and feeling of the shockwave from their explosion hit him, nearly knocking him off balance as he stumbled onto the sidewalk and leaned against one of the buildings, looking in the direction the missiles had shot and seeing smoke billowing up over the buildings.

"What the…." He gasped out, his eyes a bit wide as his thoughts were cut off by the sight and loud sounds of dozens of VTOL's speeding past him overhead, the sounds of their engines and the payloads of missiles they were unleashing onto the distance deafening him to even the sound of his own voice.

"What the hell is going on?!" He finally managed to yell out to himself, though he couldn't even hear himself say it as more and more VTOL's joined in on the assault of whatever it was that they were currently unleashing hell upon in the distance. _'Did I just arrive to this damn city just in time for a war?' _He all but yelled to himself in his mind, quickly getting his bag and getting ready to run in the opposite direction of where the hellstorm was being unleashed, only to have himself stopped by the sight of a blue Alpine screeching to a halt in the street in front of him. Watching it drift and do a complete 180 before coming to a stop, the door flying open.

"Get in! Now!" The voice left now room for argument as he ran towards the car, not about to turn down a ride in this situation and quickly realizing the woman from the picture as Misato Katsuragi, the woman who was supposed to be meeting him. Throwing his duffel bag in the car before jumping in himself, he barely had time to pull the door shut before Misato was slamming on the gas and taking off in the direction opposite of the firefight behind them.

Shinji was breathing heavily as Misato drove the car forward, quickly getting onto the highway close by and heading as fast as she could away from the destruction behind them.

"Are you okay?" Misato asked, turning to look at the boy she had just picked up near the front where everything was happening. Shinji could only turn and look at her, his face mostly blank, the only hints of what just happened was his heavy breathing.

"More or less…. Though a warzone was not something I was expecting to find upon being called by my father to this city." He said, his voice kept fairly reserved and controlled despite the adrenaline and… fear….for lack of a better word coursing through him. He wasn't sure he could feel fear anymore, at least not certain types of it. "What the hell was happening back there?"

Misato didn't waste any time in explaining to him, despite the look she had been giving him before turning back to focus on the road. "Believe me, this wasn't the ideal pick up in my books either, but don't worry, we are going somewhere safe for the moment. As for all that, that was the military's attempt at stopping the Angel."

Shinji raised an eyebrow at the Angel term, but le the subject drop. While he was extremely curious, he could only assume that it would be explained when they got wherever they were going. Right now didn't seem to be the right time to be digging for information. "I see….."

Misato turned to glance at the boy sitting in the front seat again. He was not as freaked out as she was expecting. In fact, she couldn't tell what the boy was thinking or feeling. His expression hadn't changed from that blank look on his face. It didn't matter, she would have time to talk to him on the ride down to the Geofront, right now, and she just wanted to make sure to get there in one piece.

* * *

Misato sighed out loudly as the steel doors closed tightly behind her car, feeling it shake as the wheels were locked in place and the humming around her told her that the train was getting ready to take them down to the Geofront.

"Well…" She started out, turning to look at Shinji and giving him a big smile, her personality seeming to change from the serious woman she had been on the car ride here to a much more relaxed and outgoing one. "Now that the excitement is over, I can properly introduce myself. I'm Misato Katsuragi, but please just call me Misato. It's a pleasure to finally meet you Mr. Ikari."

Shinji was caught off guard slightly by the way Misato's personality had suddenly seemed to change, but managed to cover it up fairly quickly, letting a small, albeit fake, smile cross his features. Shinji hadn't let a real smile cross his face in a long time. "Oh… Just Shinji please. And likewise Misato, though the situation certainly could have been better."

Misato could only let out a small chuckle and scratch the back of her head sheepishly. "Well, that's true, but not much we can do about it now. We'll be going someplace safe from the battle above for the moment. Though…."

Shinji watched her look around curiously as she seemed to be trying to figure out something. "Is something wrong?"

"Yeah…. We aren't moving yet. We-" She was cut off by and extremely loud sound, something that sounded like an explosion of great magnitude as the entire area shook from a massive shockwave, both her and Shinji holding onto different parts of the car for support as they rode out the quake.

"What the…. That had to be an N2 mine." Misato said, her face going back to her more serious persona as she looked to become more contemplative again.

Shinji recovered from the shockwave fairly quickly, his gaze moving back over to Misato. "An N2 mine? You mean that was…" He said looking back over the car seat at nothing but cut off as the train car began to move downwards. "That must have been why we weren't moving…." He whispered out, seeing Misato nod.

"Yes, but for them to use an N2 mine, things must not be going well for us. But still…." Her face was still serious and contemplative before she turned and looked at him again, her face suddenly going back to a smile and almost childish appearance. "Anyway, we'll get the full story when we meet your father. Did he give you some kind of pass?"

Shinji had to repress a sigh at the sudden transformation again. '_She must be with some form of the military. The need to be serious one moment, but wanting to live like herself the next? Maybe working for my father? For the good of all mankind?' _He thought the last part with sarcasm. What good could a man do for mankind if he couldn't even take care of his own son? Misato was watching him with slight interest, seeing the first forms of emotion crossing his face, surprisingly seeing it be anger before he picked up a sheet from his bag and handed it to her without a word.

"Don't like your father huh? Guess that's something we have in common." She said, causing him to look at her again, seeing a solemn look on her face. She didn't seem to be willing to push the issue for which he was thankful as he sat back and watched out the window as the shaft opened up into the Geofront, his eyes widening slightly but any form or excitement that he may have had he didn't show. "Something like that…."

Misato could only give Shinji a curious look, having expected more of a reaction out of him at seeing the Geofront. She thought she saw some excitement cross his face at first, but it didn't follow through anywhere. He wasn't acting different from the reports she was given on him, but he wasn't acting shy like she was told he would be, merely reclusive and… blank. Not the stuttering shyness she had been expecting. _'Strange kid….'_

* * *

He could have sworn that he heard the sigh that came from Misato echo throughout the area they were in. Currently they were on a movable walkway, taking them somewhere else deep into the facility, but he honestly had no idea where… nor did Misato for that matter. _'How do you get lost in your own workplace?'_

"Damnit… I could have sworn….. Why is this so complicated…?" She kept muttering as she stared at a map, trying to find the way around to wherever she was supposed to take him. He just stood there or followed her, depending on where they were at. He was fairly certain they had passed this place before and was about to bring it up when another voice caused both of them to look up at the end of the walkway.

"Misato… we don't have time for your foolishness. We are already short on manpower as it is with the Angel attacking." Said a blonde doctor who from his guess was around Misato's age as well. She was wearing a fairly standard physicians coat from the looks of things, but what caught his attention was what appeared to be a one piece bathing suit underneath.

"Ah….s-sorry Ritsuko. I still haven't memorized this place yet." Misato said with a sheepish smile as she scratched the back of her head. Shinji could only shake his head at the way the woman's personalities kept changing, but he supposed it made her unique. _'I don't really have room to talk about personality anyway.'_

He shifted his attention back to the woman in front of him, who he was assuming was a doctor. She turned and met his gaze after her own annoyed sigh at the woman beside him.

"You must be Shinji Ikari. I would say welcome and that it was nice to meet you, but seeing as how the situation is what it is, I'm going to have to cut introductions short and have you follow me. I'm Doctor Ritsuko Akagi and there is something you need to see." She spoke in a no nonsense tone before giving one last look at Misato and walking away, no doubt expecting them to follow.

"Always so stuck up Ritsuko…" Misato said with a sigh before turning to face Shinji once again. "Well, come on. She is right; there isn't really much time to be wasting."

Shinji could only repress another sigh at that statement before nodding as well and following to two women, deciding that silence would be the best answer until he figured out exactly what was going on in this place and with the battle going on above, knowing that it was still going on by the occasional light shockwave or sound in the distance, ones he guessed came from larger explosions.

He walked down a variety of corridors and walkways until they reached what he assumed their destination. The fairly relaxed atmosphere he had felt when he was just with Misato was all but gone, but considering she had gone back into her serious mode and the doctor in front of him seemed even more so, he could understand why. The next door he followed them through led them to a pitch black room, to which he followed as best as he could, stopping when the sound of footsteps in front of him stopped.

He didn't have time to think on much else before the lights flashed on, blinding him momentarily and causing him to bring his free hand up to shield his eyes as they adjusted. And once they did, he couldn't stop the small gasp from escaping his lips or keep his eyes from widening slightly. In front of him could only be described as a giant armor head. He could clearly see two spots for eyes and what appeared to be a horn and mouth plate. The whole thing was a shade of purple, but despite that, he couldn't help but think it had a menacing aspect to it.

"This is…." He started to speak out, only to stop, not sure what to think of it as he turned and looked at the women next to him once again, his face back to the blank state it had been most of the day with a hint of questioning behind it.

For her part, Ritsuko Akagi couldn't help but be slightly impressed. She expected a much different reaction from the slightly gasp and surprise that she received. This child was not like the reports the Commander had given her. It was most interesting, but she also suspected that he wouldn't be happy about seeing the child in a state different than what he was expecting.

"This is the artificial lifeform known as Evangelion Unit One. It was built here in secret and is mankind's greatest weapon, as well as its last hope. You were brought here, Shinji Ikari, as the Third Child and to be its pilot." She said as her gaze fixated upon the form of the young man in front of her, impressed or even a bit unnerved by his lack of noticeable reaction once again.

"So that's what he needed me for…." Shinji whispered out. "I knew it would be for something, but nothing like this…. I don't' even know what this is…." He whispered again, though more to himself than to the two women next to him. Judging by Misato's lack of surprise he guessed that she was aware of this fact, or had at least assumed for herself his purpose. He was about to say something to the doctor next to him when another voice decided to make itself known.

"Its been a long time, Shinji."

Shinji turned and looked up at the railing above Unit One. More lights came on and he saw the clear image of his father standing up above them all. Despite mentally preparing himself for this encounter, he couldn't prevent the anger that started boiling up inside of him as he dropped his duffel bag next to him, his gaze upon his father soon turning into a glare as his hands turned into fists as he gripped tightly, his knuckles going white.

"Father…" He let out with a bit more malice behind it than he intended. "This is what you sent for me for? To pilot something I've never seen against yet another thing I've never heard of?" Doing his best to keep his anger from flowing overboard at the man he was currently staring up at.

Misato couldn't help but be a bit shocked by the encounter. Having seen Shinji stay for the most part…emotionless on the entire way here, seeing him actually express such anger at someone caught her off guard. Her glance at Ritsuko's face told her that her friend was caught off guard as well. No doubt having read the report herself, neither expected something like this from the teenager in front of them.

Gendo stared down at his son from his position above, his face unreadable. Despite his outward appearance, the man couldn't help but be…surprised by the way his son was acting. The reports he had read over his childhood had him in a state of mind much different than this. What could have changed in the last few years since he actively read them? It looked like he may have made a mistake upon not staying caught up with his sons activities the last few years. A mistake he would correct as soon as the situation was over. "That is correct."

Shinji did his best to keep his growing anger in check. He knew it would do no good to fully lose himself at this point, but that was much easier said than done. "And how? How do you expect me to do something like this? I don't even know what is going on here!" He let out, his voice getting steadily louder towards the end.

Gendo just continued to stare down at his son. "You will be given instructions by Doctor Akagi. For the moment we just need you inside, nothing more."

He couldn't help but grit his teeth at his father's words. He wasn't prepared for a situation like this, and it was apparent to him now that he wasn't fully ready to face his father without losing himself in anger, but he could also feel the slight shockwaves from the battle above. What was he supposed to do in this situation? "Surely you have more qualified pilots than me. I don't even know what I'm supposed to be facing or what the hell is going on. I can't be your only option!"

"Our original pilot is useless at the moment, there is no one else."

'_Useless?' _Shinji thought, the way his father talked about the other pilot didn't do anything to help quell his growing anger, but he also couldn't believe he could be the only choice in this entire situation. He couldn't help but turn to Misato and see the firm look on her face as well. "You knew?"

"I didn't think you would be thrown right into the fire, but we don't' have a choice. Get inside."

He couldn't help but harden his gaze at the woman in front of him, her tone of voice completely serious like it had been in their first encounter by the station. There were only two options really in front of him, pilot for his father, or turn and leave. He couldn't believe he was the only option, but at the same time, he couldn't' help but think about if he was. _'If I walk away, I'm not better than how I was… If I stay, I'll merely be a tool for a person worse than they were….' _

His musings were brought to a close by a rough shockwave that was sent through the area, causing everyone around to slightly lose their balance and grab the railing for support. He could hear his father's voice as the shockwave started to subside.

"Its getting close…. It must be able to sense us…"

Shinji looked back up at his father just in time to see the elder Ikari meet his unflinching gaze. Before Shinji could speak another word, his father beat him to it.

"If you are going to do, do it now. If not, then leave."

Shinji could feel his whole body tense at the statement. Not seconds after his father's statement did he hear a door opening, looking to the sound along with the two women next to him, he saw the doors on the far end of the walkway opening, a medical crew with a stretcher bringing in what looked to be a severely wounded girl. She looked like she could barely breathe, let alone doing anything else. It didn't take him long to realize this must have been the other pilot. '_You call her useless….for that? Damn you father…. Damnit….'_

His shoulders sagged down slightly as he felt his anger rise, but his ability to fight in this situation diminish. He missed his father's smirk that the sight of him doing so, his focus on the girl and then the Evangelion in front of him. Looking around, he could see everyone looking at him expectantly, waiting for his answer.

"You're being used again Shinji…." He whispered out, his mind being made up as he felt he had no choice, looking back up at his father and missing the questioning looks from both Misato and Ritsuko, both having heard his whisper. "Fine. I'll pilot it."

His voice even sounded defeated to him, and he hated it. He almost sounded like he did back then, a way he swore to never sound again. He wouldn't let this happen to him again, he couldn't.

Ritsuko gave him a look before nodding herself, turning around and yelling instructions out to the maintenance crew around them, leaving Misato standing next to him, his father turning and leaving above them as soon as the words had left his mouth.

Misato looked at him before brining and hand up and placing it on his shoulder. The older woman looked down at him with mixed emotions. She truly wasn't sure what to think of the boy, and even less of what she had heard him whisper mere moments before. '_There's definitely more to you than meets the eye… Shinji Ikari.'_

* * *

It was a blur of motion after that to Shinji. He quickly found himself sitting in what they called the Entry Plug to the Evangelion, sitting with controls on either side of him just within arm's reach. He could hear the chatter of everyone around him, each talking about different things as he felt the Plug moved to be entered into the Evangelion. He couldn't help but look around and be slightly amazed, his anger from the confrontation with his father fading as his curiosity and focus on the current situation grew.

"Okay Shinji…" The voice of Doctor Akagi coming over the intercom as the others were drown out, probably by them. "There isn't much time to go over all of the aspects of the Evangelion, but I'm going to give you the basics, so listen closely…"

Shinji continued to feel the motion of the plug as he listened to the doctor's instructions. About how the gear on his head linked his mind to the Evangelion he was being put into and that he had to think to move it. That along with the controls he had in his hands, but she told him to focus on the thinking part. He kept his face in the same empty state he had had it most of the day as he listened and watched as his plug was inserted. Seeing numerous visuals and colors appear around him in slight aw before becoming a crystal clear image of the catwalk he was just on as well as the rest of the cage around him.

"Whoa…" He couldn't help but let out an impressed gasp, letting his mouth hang open for a second before pulling himself back together as he focused again on the instructions that Misato and Ritsuko were both feeding to him.

"Okay… I think I've got it…" He responded, feeling the own nervousness in his voice, but also steeling himself for what was to come as he watch the catwalk pull away, amazed that he could actually feel the restraints being released, not just from the slight shaking but also from the feeling of the pressure on his arms disappearing. '_I really do feel everything…. This could be really bad….'_

He couldn't help but feel even more nervous as the Evangelion was locked in place at the shaft where he would be launched up, hearing Misato going over everyone in the Command Center and making sure they were all ready for what was to come before hearing her redirect her voice to him. "Are you ready Shinji?"

He could only give a nod to the visual screen in front of him with Misato's face in it. She returned the nod, offering a small smile before turning serious again. "Okay then. Begin the Operation! Evangelion Unit One… Launch!"

Shinji braced himself for the G-forces that he was told would hit him, feeling it bare down on his body as he shot up to the surface and prepared himself for whatever he was about to face, already realizing that they had given him info on how to pilot, but none on the actual enemy. '_Looks like it's going to be more of a fight to keep my promise than I thought…. But I will keep it…' _He thought as he suddenly came to an abrupt stop, the door folding down quickly in front of him as the cage around him fell away, leaving him standing right in front of a creature with eyes that seemed to glow red as it turned to face him. He forced back his surprise at the sight of the creature in exchange for reviewing everything quickly in his head that the Doctor had told him, bracing himself for what was about to happen. '_Give me strength…Maki…'_

**To be continued…**

**A/N: Like I said, this idea has been going around in my head for a while and I'm just now finding time to write it down with one of my harder semesters being over. I forgot to mention above, but all the children will be 16 in this fic. The ages of the other characters will remain the same unless something arises that forces me to change them. The children's ages were changed for the sake of Shinji's past. It's going to play a major role in this story and most of the story is going to focus on Shinji in general. I know the beginning is a little rough, and honestly I will probably come back and edit a bit in the future as I settle in and get the characters and my style more fleshed out as well as any mishaps someone may point out in a review. Anyway, I look forward to hearing from all those that enjoy this story, and feel free to PM or drop me any questions. Until next time.**


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